I believe this thread should have been made a long time ago, and should be sticked, at least for the new users, so here it goes:

1) As everyone already knows, CIA files are to be installed using DevMenu (or BigBlueMenu), preferably the latest version (v6.20 as of Nov. 2014). 2) These CIA files ARE and MUST be installed to the emuNAND using GateWay (and I'm putting aside the ones that use CFW here). Of course, sysNAND is off limits... 3) Also, the following methods also fix the well known "unwrapping gift bug". This happens when you use the "same" sysNAND and emuNAND.

WHEN UNSURE, ALWAYS KEEP AN UPDATED BACKUP OF YOUR EMUNAND AT HAND! Meaning: Backup all the content of the SD card that you can see in Windows, AND use emuNANDTool to extract the emuNAND partition from the SD card and keep it safe.

Now comes the tricky parts...

4) AT NO CIRCUNSTANCE YOU MUST ACCESS THE "DATA MANAGEMENT" SECTION OF THE "CONSOLE DEFINITIONS" IN THE SYSNAND! By doing so, YOU WILL LOSE EVERY CIA INSTALLED AND IT'S SAVE DATA ALL TOGETHER. So for those that have Pokemon installed in emuNAND, BEWARE! Also, THERE IS NO KNOWN WAY TO BLOCK THIS ACCESS (Parental Control has no option to lock this out like it has to Updates...) so be VERY CAUTIOUS when accessing the GateWay loader process... or... USE TWO SD CARDS! More detailed in the Extra Notes section down below...

5) To install any CIA, you MUST at least have a SD Card (SD or miniSD with adapter (trust me, it works)) with at least the DOUBLE of the size of the CIA. This means: If you want to install a game that has a CIA with 2GB, you must have at least 4GB of free space in your card to install it. This is because you need the space for the CIA AND to install the game. After installing the game, you can safely delete the CIA file, either using DevMenu or in Windows (preffered).

6) Take caution about the Unique ID's of each CIA. Meaning: each CIA has it's own Unique ID. If you manage to, even by accident, install a CIA that has the same Unique ID of a CIA that you had already installed, the new CIA will replace the old one, even if it was a COMPLETELY different game or application. So take caution about this. This can easily happen if no precautions are made.

7) Accessing the eShop in emuNAND WILL NOT delete your installed CIA's. However, since you have to login in the "Nintendo Network", this will DELETE, together with your installed themes, all the DLCs and/or Mii Plaza paid titles that you have. (Thanks wimzie) Also, the following reports have been made: a) Sunny Delacote Boundarius:"i can tell that when you enter to the eshop with cia installed, they take it as if you bought the game." b) Quicksilver88 has reported that, infact accessing the eShop will not delete any CIA installed, however, if you try to update said CIA installation with a newer more recent version that's available in the eShop, at the end of the install, the eShop installation will fail (most probably it will check if you indeed have bought the application, since it checks that you didn't, it cancels the update, and gives an error...)

That said, I advice access to the eShop ONLY by using the 2 SD Card method, and I can't stress this enough: Access the eShop at your own risk!

8) Logging in the Nintendo Network (either by eShop or Pokemon Bank, etc...) in emuNAND WILL DELETE your current themes, all the DLCs and/or Mii Plaza paid titles (if this theme was a CIA install, of course...). Apps won't be deleted though.

9) ????????

10) PROFIT!

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Extra Notes:

1) If you take your SD Card out the side of your 3DS and your Gateway card out and format your 3DS sysNAND and start over again, this will separate your two NANDs, so going to Data Management and erasing files from there will not cause your CIA installed files to delete from then on. HOWEVER, this will stop SD decrypter from working. (Special Thanks to: reecey & LostPants)

or...

USE TWO SD CARDS: (Special Thanks to Reecey for this method...)

In order to safely access the Data Management of the sysNAND without losing everything from the emuNAND, one must perform a FORMAT to the 3DS! BUT, TO BE ABLE TO DO THIS WITHOUT LOSING THE SD DECRYPTER ABILITY, HERE GOES:

ATTENTION: THIS ONLY APPLIES TO SYSTEMS THAT DO NOT HAVE ANY BOUGHT GAMES IN SYSNAND AND EMUNAND (ex: you never bought any game in sysNAND or new console without games...) If you bought any game, have not decrypted it, and you have it in emuNAND, you can't format the 3DS, or else, the sysNAND will change, and you will lose access to decrypt the game, since the XOR's will change. Side note: Not shure about this but: supposedly, if you bought the game in sysNAND, and format your 3DS, if you try to access the eShop and vinculate your 3DS again, it's supposed to be able to and then you can download your bought games again, but I'm not shure about this so, better not take the risk...

1) Remove your SD Card and Gateway card from your 3DS, and FORMAT THE CONSOLE. This will make your sysNAND be different from your emuNAND, thus losing the problem of deletion. 2) Now, with ANOTHER SD card, install the GateWay exploit AND emuNAND to the latest version (so that you can have access to the eShop). 3) By doing this, your SD Decrypter will work normally BUT ONLY USING THIS NEW SD CARD AND THIS NEW EMUNAND! So, if you plan on buying something in the eShop (and decrypting it to share it or to install it in the OTHER emuNAND), you will always be able to using this emuNAND. 4) Use the oldest emuNAND to play only! And that's that! Two problems solved. One card to access eShop and buy/decrypt stuff, other SD Card to play decrypted stuff without worries of deletion from the sysNAND!

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For now, I guess that's all. Hope this little "guide" helps someone out.

A Big Special Thanks to everyone that took the risks and helped out gattering the information present in this post.